script_tricks
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script_tricks [2013/02/13 13:48] rdiazgar |
script_tricks [2014/02/16 20:08] (current) rdiazgar |
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| - | ====== Script Tricks ====== | + | ====== Job Parameters ====== |
| - | + | Here's the meaning of useful parameters that we can add in the header of our job scripts. You can either add them on the header of a script or directly in the qsub command. | |
| - | Here's the meaning of useful parameters that we can add in the header of our job scripts. | + | |
| <code> | <code> | ||
| #$ -N NAME = Names our job in the cluster as specified in NAME | #$ -N NAME = Names our job in the cluster as specified in NAME | ||
| #$ -q QUEUE = Automatically sends our job to the specified queue in QUEUE, so we don't need to specify it in the qsub command. | #$ -q QUEUE = Automatically sends our job to the specified queue in QUEUE, so we don't need to specify it in the qsub command. | ||
| - | #$ -M EMAIL = Sends notifications of the job status to the specified address in EMAIL, according to criteria below | + | #$ -M EMAIL = Sends notifications of the job status to the specified address in EMAIL, according to criteria below. |
| - | #$ -m beas = Send you email of job status (b)egin, (e)rror, (a)bort, (s)suspend | + | #$ -m beas = Send you email of job status (b)egin, (e)rror, (a)bort, (s)suspend. |
| + | #$ -e DIRNAME = redirects error logs to DIRNAME. Default is home directory | ||
| + | #$ -o DIRNAME = redirects standard output to DIRNAME. Default is home directory. | ||
| + | #$ -l hostname=HNAME = forces queue to submit job in the specified HNAME (cronus, rhea, etc...). | ||
| </code> | </code> | ||
| - | Sample header for some script myscript.sh: | + | |
| + | Sample header for hello_world.sh: | ||
| <code> | <code> | ||
| - | #!/bin/csh | + | #!/bin/bash |
| # | # | ||
| - | #$ -N parsedisco | + | #$ -N hello_world |
| #$ -M someaddress@uci.edu | #$ -M someaddress@uci.edu | ||
| #$ -m beas | #$ -m beas | ||
| #$ -q ttn.q | #$ -q ttn.q | ||
| + | |||
| + | echo "hello world" | ||
| </code> | </code> | ||
| - | more info at http://hpc.oit.uci.edu/running-jobs | + | Another way to do it is by removing the #$ parameters of the header and run: |
| + | |||
| + | <code> | ||
| + | qsub -N hello_world -M someaddress@uci.edu -m beas -q ttn.q hello_world.sh | ||
| + | </code> | ||
| ====== Log files ====== | ====== Log files ====== | ||
| - | Another cool thing from SGE is that it automatically creates a log file in the folder where you make the qsub call, and leaves two log files, JOBNAME.eJOBID and JOBNAME.oJOBID. 'e' is for error messages and 'o' is for standard output. | + | SGE automatically creates 2 log files in the default/specified folder, JOBNAME.eJOBID and JOBNAME.oJOBID. 'e' is for error messages and 'o' is for standard output. |
script_tricks.1360792082.txt.gz · Last modified: 2013/02/13 13:48 by rdiazgar
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